I wouldn't recommend letting any mod overwrite another mod's version of the Commands cfg files, unless you know for certain that the new version is compatible with both mods. If not, you're going to lose entries in those files that are required for the proper working of one mod or the other.
Many mods that use those files include instructions for manually editing your existing ones to include what they need without overwriting what you already have.
Once you get the hang of it, it's not that difficult to compare different versions of those files, and do the manual editing that will include everything each mod needs. (Unless they use commands that conflict with each other, which is something I haven't encountered so far *knock wood*).
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